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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:23:54 +0000
parents 85edbb7a436b
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5:85edbb7a436b 6:fcadded98e61
1 <tool id="ip_convertimage" name="Convert image format" version="6.7.0+galaxy2"> 1 <tool id="ip_convertimage" name="Convert image format" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>with Bioformats</description> 2 <description>with Bioformats</description>
3 <edam_operations> 3 <macros>
4 <edam_operation>operation_3443</edam_operation> 4 <import>creators.xml</import>
5 </edam_operations> 5 <import>tests.xml</import>
6 <xrefs> 6 <token name="@TOOL_VERSION@">6.7.0</token>
7 <xref type="biii">python-bioformats</xref> 7 <token name="@VERSION_SUFFIX@">3</token>
8 </xrefs> 8 </macros>
9 <requirements> 9 <creator>
10 <requirement type="package" version="6.7.0">bftools</requirement> 10 <expand macro="creators/alliecreason"/>
11 </requirements> 11 <expand macro="creators/bmcv"/>
12 <command> 12 </creator>
13 <edam_operations>
14 <edam_operation>operation_3443</edam_operation>
15 </edam_operations>
16 <xrefs>
17 <xref type="biii">python-bioformats</xref>
18 </xrefs>
19 <requirements>
20 <requirement type="package" version="@TOOL_VERSION@">bftools</requirement>
21 </requirements>
22 <command>
13 <![CDATA[ 23 <![CDATA[
14 bfconvert 24 bfconvert
15 #if $series_options['extract'] == 'True' 25 #if $series_options['extract'] == 'True'
16 -series $series_options.series 26 -series $series_options.series
17 #end if 27 #end if
43 -compression $compression 53 -compression $compression
44 #end if 54 #end if
45 '$input_file' './res.$out_format' && 55 '$input_file' './res.$out_format' &&
46 mv './res.$out_format' ./result_image 56 mv './res.$out_format' ./result_image
47 ]]> 57 ]]>
48 </command> 58 </command>
49 <inputs> 59 <inputs>
50 <param label="Input Image" name="input_file" type="data" format="atsf,scn,ali,labels,ffr,jpeg,ndpi,tf8,pty,fff,mnc,vms,mng,xml,pcx,img,pct,ims,bip,ome.xml,bin,flex,his,hdr,mov,psd,spi,ipl,dv,aiix,j2kr,pst,mod,ome.tif,tif,obf,dib,dic,im3,tga,pbm,c01,crw,mrcs,l2d,seq,mdb,cfg,htm,mvd2,arf,vsi,companion.ome,htd,aim,fts,ndpis,r3d.log,nef,res,jpx,ics,rec,nd2,cr2,dcm,mea,ome,lei,lms,j2k,oib,mtb,ima,ets,wlz,pict,sm3,sm2,nrrd,xdce,acff,al3d,zvi,1sc,xys,tiff,pgm,pcoraw,ppm,ipm,set,cxd,ipw,apl,fake,tnb,txt,xv,tf2,ps,log,zip,epsi,j2ki,dicom,top,msr,frm,hed,gif,dm2,dm3,dm4,zpo,wav,wat,2fl,sdt,liff,hx,pic,ome.btf,am,bmp,pnl,r3d_d3d,jpf,png,tfr,dti,nii.gz,cif,fdf,grey,df3,stk,fli,hdf,btf,stp,ch5,v,sld,ids,dv.log,jpk,mrw,r3d,xlog,ano,jpe,sxm,jpg,vws,raw,czi,spl,avi,ome.tf8,inf,spc,ome.tf2,spe,lsm,afm,lif,naf,afi,inr,lim,nd,tim,html,sif,env,tif,csv,map,nii,gel,ome.tiff,oif,par,amiramesh,pr3,fits,lut,jp2,oir,dat,aisf,zfr,zfp,xqd,eps,xqf,st,nhdr,i2i,thm,exp,svs,mrc"/> 60 <param label="Input Image" name="input_file" type="data" format="atsf,scn,ali,labels,ffr,jpeg,ndpi,tf8,pty,fff,mnc,vms,mng,xml,pcx,img,pct,ims,bip,ome.xml,bin,flex,his,hdr,mov,psd,spi,ipl,dv,aiix,j2kr,pst,mod,ome.tif,tif,obf,dib,dic,im3,tga,pbm,c01,crw,mrcs,l2d,seq,mdb,cfg,htm,mvd2,arf,vsi,companion.ome,htd,aim,fts,ndpis,r3d.log,nef,res,jpx,ics,rec,nd2,cr2,dcm,mea,ome,lei,lms,j2k,oib,mtb,ima,ets,wlz,pict,sm3,sm2,nrrd,xdce,acff,al3d,zvi,1sc,xys,tiff,pgm,pcoraw,ppm,ipm,set,cxd,ipw,apl,fake,tnb,txt,xv,tf2,ps,log,zip,epsi,j2ki,dicom,top,msr,frm,hed,gif,dm2,dm3,dm4,zpo,wav,wat,2fl,sdt,liff,hx,pic,ome.btf,am,bmp,pnl,r3d_d3d,jpf,png,tfr,dti,nii.gz,cif,fdf,grey,df3,stk,fli,hdf,btf,stp,ch5,v,sld,ids,dv.log,jpk,mrw,r3d,xlog,ano,jpe,sxm,jpg,vws,raw,czi,spl,avi,ome.tf8,inf,spc,ome.tf2,spe,lsm,afm,lif,naf,afi,inr,lim,nd,tim,html,sif,env,tif,csv,map,nii,gel,ome.tiff,oif,par,amiramesh,pr3,fits,lut,jp2,oir,dat,aisf,zfr,zfp,xqd,eps,xqf,st,nhdr,i2i,thm,exp,svs,mrc"/>
51 <param name="out_format" type="select" label="Output data type"> 61 <param name="out_format" type="select" label="Output data type">
52 <option value="tiff" selected="True">TIFF</option> 62 <option value="tiff" selected="True">TIFF</option>
53 <option value="png">PNG</option> 63 <option value="png">PNG</option>
54 <option value="jpg">JPEG</option> 64 <option value="jpg">JPEG</option>
55 <option value="ome.tiff">OME TIFF</option> 65 <option value="ome.tiff">OME TIFF</option>
56 <option value="jp2">JPEG 2000</option> 66 <option value="jp2">JPEG 2000</option>
57 <option value="eps">EPS</option> 67 <option value="eps">EPS</option>
58 <option value="avi">AVI</option> 68 <option value="avi">AVI</option>
59 </param>
60
61 <conditional name="series_options">
62 <param label="Extract series" name="extract" type="select">
63 <option selected="True" value="False">All series</option>
64 <option value="True">Extract series</option>
65 </param> 69 </param>
66 <when value="False"> </when> 70
67 <when value="True"> 71 <conditional name="series_options">
68 <param name="series" type="integer" value="0" label="Series id" /> 72 <param label="Extract series" name="extract" type="select">
69 </when> 73 <option selected="True" value="False">All series</option>
70 </conditional> 74 <option value="True">Extract series</option>
71 <conditional name="timepoint_options"> 75 </param>
72 <param name="extract" type="select" label="Extract timepoint"> 76 <when value="False"> </when>
73 <option selected="True" value="False">All timepoints</option> 77 <when value="True">
74 <option value="True">Extract timepoint</option> 78 <param name="series" type="integer" value="0" label="Series id" />
75 </param> 79 </when>
76 <when value="False"></when> 80 </conditional>
77 <when value="True"> 81 <conditional name="timepoint_options">
78 <param name="timepoint" type="integer" value="0" label="Timepoint ID" /> 82 <param name="extract" type="select" label="Extract timepoint">
79 </when> 83 <option selected="True" value="False">All timepoints</option>
80 </conditional> 84 <option value="True">Extract timepoint</option>
81 <conditional name="channel_options"> 85 </param>
82 <param name="extract" type="select" label="Extract channel" > 86 <when value="False"></when>
83 <option selected="True" value="False">All channels</option> 87 <when value="True">
84 <option value="True">Extract channel</option> 88 <param name="timepoint" type="integer" value="0" label="Timepoint ID" />
85 </param> 89 </when>
86 <when value="False"> </when> 90 </conditional>
87 <when value="True"> 91 <conditional name="channel_options">
88 <param name="channel" type="integer" value="0" label="Channel id" /> 92 <param name="extract" type="select" label="Extract channel" >
89 </when> 93 <option selected="True" value="False">All channels</option>
90 </conditional> 94 <option value="True">Extract channel</option>
91 <conditional name="z_options"> 95 </param>
92 <param label="Extract z-slice" name="extract" type="select"> 96 <when value="False"> </when>
93 <option selected="True" value="False">All z-slices</option> 97 <when value="True">
94 <option value="True">Extract z-slice</option> 98 <param name="channel" type="integer" value="0" label="Channel id" />
95 </param> 99 </when>
96 <when value="False"> </when> 100 </conditional>
97 <when value="True"> 101 <conditional name="z_options">
98 <param name="z" type="integer" value="0" label="Z-slice id" /> 102 <param label="Extract z-slice" name="extract" type="select">
99 </when> 103 <option selected="True" value="False">All z-slices</option>
100 </conditional> 104 <option value="True">Extract z-slice</option>
101 <conditional name="range_options"> 105 </param>
102 <param label="Extract range" name="extract" type="select"> 106 <when value="False"> </when>
103 <option selected="True" value="False">All images</option> 107 <when value="True">
104 <option value="True">Extract range by indicess (inclusive)</option> 108 <param name="z" type="integer" value="0" label="Z-slice id" />
105 </param> 109 </when>
106 <when value="False"> </when> 110 </conditional>
107 <when value="True"> 111 <conditional name="range_options">
108 <param name="range_lower" type="integer" value="0" label="Lower image id" /> 112 <param label="Extract range" name="extract" type="select">
109 <param name="range_upper" type="integer" value="1" label="Upper image id" /> 113 <option selected="True" value="False">All images</option>
110 </when> 114 <option value="True">Extract range by indicess (inclusive)</option>
111 </conditional> 115 </param>
112 <conditional name="crop_options"> 116 <when value="False"> </when>
113 <param label="Extract crop" name="extract" type="select"> 117 <when value="True">
114 <option selected="True" value="False">Full image</option> 118 <param name="range_lower" type="integer" value="0" label="Lower image id" />
115 <option value="True">Extract crop</option> 119 <param name="range_upper" type="integer" value="1" label="Upper image id" />
116 </param> 120 </when>
117 <when value="False"> </when> 121 </conditional>
118 <when value="True"> 122 <conditional name="crop_options">
119 <param name="crop_x" type="integer" value="0" label="X" /> 123 <param label="Extract crop" name="extract" type="select">
120 <param name="crop_y" type="integer" value="0" label="Y" /> 124 <option selected="True" value="False">Full image</option>
121 <param name="crop_width" type="integer" value="512" label="Width" /> 125 <option value="True">Extract crop</option>
122 <param name="crop_height" type="integer" value="512" label="height" /> 126 </param>
123 </when> 127 <when value="False"> </when>
124 </conditional> 128 <when value="True">
125 <conditional name="tile_options"> 129 <param name="crop_x" type="integer" value="0" label="X" />
126 <param label="Tile image" name="extract" type="select"> 130 <param name="crop_y" type="integer" value="0" label="Y" />
127 <option selected="True" value="False">No tiling</option> 131 <param name="crop_width" type="integer" value="512" label="Width" />
128 <option value="True">Tile image</option> 132 <param name="crop_height" type="integer" value="512" label="height" />
129 </param> 133 </when>
130 <when value="False"> </when> 134 </conditional>
131 <when value="True"> 135 <conditional name="tile_options">
132 <param name="tile_x" type="integer" value="512 " label="Tile width" /> 136 <param label="Tile image" name="extract" type="select">
133 <param name="tile_y" type="integer" value="512 " label="Tile height" /> 137 <option selected="True" value="False">No tiling</option>
134 </when> 138 <option value="True">Tile image</option>
135 </conditional> 139 </param>
136 <conditional name="pyramid_options"> 140 <when value="False"> </when>
137 <param label="Pyramid image" name="generate" type="select" help="Pyramids will be generated only if the selected output format supports pyramids (OME TIFF, JPEG 2000)."><!-- see: https://docs.openmicroscopy.org/bio-formats/6.7.0/supported-formats.html --> 141 <when value="True">
138 <option selected="True" value="True">Generate Pyramid</option> 142 <param name="tile_x" type="integer" value="512 " label="Tile width" />
139 <option value="False">No Pyramid</option> 143 <param name="tile_y" type="integer" value="512 " label="Tile height" />
140 </param> 144 </when>
141 <when value="True"> 145 </conditional>
142 <param name="pyramid_resolutions" type="integer" value="4" label="Pyramid Resolutions"/> 146 <conditional name="pyramid_options">
143 <param name="pyramid_scale" type="integer" value="2" label="Pyramid Scale" /> 147 <param label="Pyramid image" name="generate" type="select" help="Pyramids will be generated only if the selected output format supports pyramids (OME TIFF, JPEG 2000)."><!-- see: https://docs.openmicroscopy.org/bio-formats/6.7.0/supported-formats.html -->
144 </when> 148 <option selected="True" value="True">Generate Pyramid</option>
145 <when value="False" /> 149 <option value="False">No Pyramid</option>
146 </conditional> 150 </param>
147 <param name="bigtiff" label="Big TIFF" type="boolean" checked="false" truevalue="-bigtiff" falsevalue=""/> 151 <when value="True">
148 <param name="noflat" label="No Flatten" type="boolean" checked="true" truevalue="-noflat" falsevalue=""/> 152 <param name="pyramid_resolutions" type="integer" value="4" label="Pyramid Resolutions"/>
149 <param label="Compression" name="compression" type="select"> 153 <param name="pyramid_scale" type="integer" value="2" label="Pyramid Scale" />
150 <option selected="True" value="False">No Compression</option> 154 </when>
151 <option value="LZW">LZW</option> 155 <when value="False" />
152 <option value="JPEG-2000">JPEG-2000</option> 156 </conditional>
153 <option value="JPEG-2000 Lossy">JPEG-2000 Lossy</option> 157 <param name="bigtiff" label="Big TIFF" type="boolean" checked="false" truevalue="-bigtiff" falsevalue=""/>
154 <option value="JPEG">JPEG</option> 158 <param name="noflat" label="No Flatten" type="boolean" checked="true" truevalue="-noflat" falsevalue=""/>
155 <option value="zlib">zlib</option> 159 <param label="Compression" name="compression" type="select">
156 </param> 160 <option selected="True" value="False">No Compression</option>
157 </inputs> 161 <option value="LZW">LZW</option>
158 <outputs> 162 <option value="JPEG-2000">JPEG-2000</option>
159 <data format="tiff" name="output" from_work_dir="result_image"> 163 <option value="JPEG-2000 Lossy">JPEG-2000 Lossy</option>
160 <change_format> 164 <option value="JPEG">JPEG</option>
161 <when input="out_format" value="tiff" format="tiff" /> 165 <option value="zlib">zlib</option>
162 <when input="out_format" value="png" format="png" /> 166 </param>
163 <when input="out_format" value="jpg" format="jpg" /> 167 </inputs>
164 <when input="out_format" value="ome.tiff" format="ome.tiff" /> 168 <outputs>
165 <when input="out_format" value="jp2" format="jpg" /> 169 <data format="tiff" name="output" from_work_dir="result_image">
166 <when input="out_format" value="eps" format="eps" /> 170 <change_format>
167 <when input="out_format" value="avi" format="avi" /> 171 <when input="out_format" value="tiff" format="tiff" />
168 </change_format> 172 <when input="out_format" value="png" format="png" />
169 </data> 173 <when input="out_format" value="jpg" format="jpg" />
170 </outputs> 174 <when input="out_format" value="ome.tiff" format="ome.tiff" />
171 <tests> 175 <when input="out_format" value="jp2" format="jpg" />
176 <when input="out_format" value="eps" format="eps" />
177 <when input="out_format" value="avi" format="avi" />
178 </change_format>
179 </data>
180 </outputs>
181 <tests>
172 <test> 182 <test>
173 <param name="input_file" value="input.png" /> 183 <param name="input_file" value="input.png" />
174 <param name="out_format" value="tiff" /> 184 <param name="out_format" value="tiff" />
175 <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/> 185 <expand macro="tests/intensity_image_diff" name="output" value="res.tiff" ftype="tiff"/>
176 </test> 186 </test>
177 <test> 187 <test>
178 <param name="input_file" value="input.png" /> 188 <param name="input_file" value="input.png" />
179 <param name="out_format" value="ome.tiff" /> 189 <param name="out_format" value="ome.tiff" />
180 <conditional name="pyramid_options"> 190 <conditional name="pyramid_options">
181 <param name="generate" value="True"/> 191 <param name="generate" value="True"/>
182 <param name="pyramid_resolutions" value="4"/> 192 <param name="pyramid_resolutions" value="4"/>
183 <param name="pyramid_scale" value="2"/> 193 <param name="pyramid_scale" value="2"/>
184 </conditional> 194 </conditional>
185 <output name="output" value="res.ome.tiff" ftype="ome.tiff" compare="sim_size"/> 195 <expand macro="tests/intensity_image_diff" name="output" value="res.ome.tiff" ftype="ome.tiff"/>
186 </test> 196 </test>
187 <test> 197 <test>
188 <param name="input_file" value="input.tiff" /> 198 <param name="input_file" value="input.tiff" />
189 <param name="out_format" value="png" /> 199 <param name="out_format" value="png" />
190 <output name="output" value="input.tiff.png" ftype="png" compare="sim_size"/> 200 <expand macro="tests/intensity_image_diff" name="output" value="input.tiff.png" ftype="png"/>
191 </test> 201 </test>
192 </tests> 202 </tests>
193 <help> 203 <help>
194 **What it does** 204
195 205 **Converts image format.**
196 Universial image converter using bioformats. 206
207 Universial image converter using bioformats.
208
197 </help> 209 </help>
198 <citations> 210 <citations>
199 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 211 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
200 </citations> 212 </citations>
201 </tool> 213 </tool>